{"doi":"10.1186/1748-7188-6-7","title":"An experimental study of Quartets MaxCut and other supertree methods","abstract":null,"journal":"Algorithms for Molecular Biology","year":2011,"id":590844,"datarank":1.4600682596185997,"base_score":3.828641396489095,"endowment":3.828641396489095,"self_citation_contribution":0.5742962094733643,"citation_network_contribution":0.8857720501452352,"self_endowment_contribution":0.5742962094733643,"citer_contribution":0.8857720501452352,"corpus_percentile":null,"corpus_rank":null,"citation_count":45,"citer_count":30,"citers_with_citation_signal":23,"citers_with_endowment":23,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1511633,"name":"Rahul Suri","orcid":null,"position":1,"is_corresponding":false},{"id":1511634,"name":"C Randal Linder","orcid":null,"position":2,"is_corresponding":false},{"id":58699,"name":"Tandy Warnow","orcid":"0000-0001-7717-3514","position":3,"is_corresponding":false},{"id":1511632,"name":"M Shel Swenson","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"An experimental study of Quartets MaxCut and other supertree methods","abstract":"BACKGROUND: Supertree methods represent one of the major ways by which the Tree of Life can be estimated, but despite many recent algorithmic innovations, matrix representation with parsimony (MRP) remains the main algorithmic supertree method. RESULTS: We evaluated the performance of several supertree methods based upon the Quartets MaxCut (QMC) method of Snir and Rao and showed that two of these methods usually outperform MRP and five other supertree methods that we studied, under many realistic model conditions. However, the QMC-based methods have scalability issues that may limit their utility on large datasets. We also observed that taxon sampling impacted supertree accuracy, with poor results obtained when all of the source trees were only sparsely sampled. Finally, we showed that the popular optimality criterion of minimizing the total topological distance of the supertree to the source trees is only weakly correlated with supertree topological accuracy. Therefore evaluating supertree methods on biological datasets is problematic. CONCLUSIONS: Our results show that supertree methods that improve upon MRP are possible, and that an effort should be made to produce scalable and robust implementations of the most accurate supertree methods. Also, because topological accuracy depends upon taxon sampling strategies, attempts to construct very large phylogenetic trees using supertree methods should consider the selection of source tree datasets, as well as supertree methods. Finally, since supertree topological error is only weakly correlated with the supertree's topological distance to its source trees, development and testing of supertree methods presents methodological challenges.","is_dataset_classified":null,"base_score":3.828641396489095,"endowment":3.828641396489095,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"21504600","pmcid":"PMC3101644","openalex_id":"https://openalex.org/W2118058771","authors":[],"funders":[{"funder_name":"National Science Foundation","grant_id":"0114387","title":"IGERT: Computational Phylogenetics and Applications to Biology"},{"funder_name":"National Science Foundation","grant_id":"0733029","title":"Collaborative Research: Large-scale simultaneous multiple alignment and phylogeny estimation"},{"funder_name":"National Science Foundation","grant_id":"0331453","title":"Information Technology Research (ITR): Building the Tree of Life -- A National Resource for Phyloinformatics and Computational Phylogenetics"}],"total_grants":3,"fwci":2.3113,"citation_percentile":0.88815043,"influential_citations":0,"citation_trend":[{"year":2012,"count":4},{"year":2013,"count":4},{"year":2014,"count":6},{"year":2015,"count":1},{"year":2016,"count":4},{"year":2017,"count":2},{"year":2018,"count":7},{"year":2019,"count":3},{"year":2020,"count":1},{"year":2021,"count":3},{"year":2022,"count":1},{"year":2023,"count":1},{"year":2024,"count":2},{"year":2025,"count":1}],"oa_status":"gold","license":"CC BY","oa_locations":[{"url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-7","host_type":"journal"},{"url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-6-7","host_type":"publisher"},{"url":"http://link.springer.com/content/pdf/10.1186/1748-7188-6-7.pdf","host_type":"publisher"},{"url":"http://link.springer.com/article/10.1186/1748-7188-6-7/fulltext.html","host_type":"publisher"},{"url":"https://doi.org/10.1186/1748-7188-6-7","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/21504600","host_type":"repository"},{"url":"https://doaj.org/article/bde227e6f74546cd8a3ae47dac19028d","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3101644","host_type":"repository"},{"url":"http://hdl.handle.net/2152/27804","host_type":"repository"},{"url":"http://www.almob.org/content/pdf/1748-7188-6-7.pdf","host_type":"BioMedCentral"},{"url":"http://www.almob.org/content/6/1/7/abstract","host_type":"BioMedCentral"},{"url":"https://europepmc.org/articles/PMC3101644","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3101644?pdf=render","host_type":"Europe_PMC"},{"url":"https://almob.biomedcentral.com/track/pdf/10.1186/1748-7188-6-7","host_type":""},{"url":"https://doi.org/10.1007/978-3-642-15294-8_24","host_type":""},{"url":"https://repositories.lib.utexas.edu/bitstream/2152/27804/1/1748-7188-6-7.pdf","host_type":""},{"url":"http://dx.doi.org/10.1186/1748-7188-6-7","host_type":""},{"url":"https://dx.doi.org/10.1186/1748-7188-6-7","host_type":""},{"url":"https://dx.doi.org/10.1007/978-3-642-15294-8_24","host_type":""},{"url":"https://doi.org/https://doi.org/10.1186/1748-7188-6-7","host_type":""}],"fields_of_study":["Genomics and Phylogenetic Studies","Genomics and Chromatin Dynamics","Gene expression and cancer classification","0301 basic medicine","0206 medical engineering","02 engineering and technology","03 medical and health sciences"],"mesh_terms":[],"keywords":["Supertree","Computer science","Scalability","Tree (set theory)","Algorithm","Limit (mathematics)","Theoretical computer science","Phylogenetic tree","Data mining","Topology (electrical circuits)","Mathematics","Combinatorics","Biology","QH301-705.5","Applied Mathematics","Research","MRP","Quartets MaxCut","QH426-470","Supertree methods","Computational Theory and Mathematics","Structural Biology","518","Genetics","Biology (General)","Molecular Biology"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"No poverty"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-25T12:40:11.274793Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}